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The four study lakes (Figure 1) are Lake Chad, Victoria, Tanganyika, and Lake Malawi/Nyasa/Niasa (LMNN). Lake Chad is one of the world’s most important agricultural heritage sites, providing a lifeline to nearly 30 million people in four riparian countries (Cameroun, Chad, Niger, and Nigeria) in West Africa. There are reports of it having experienced a significant decline in lake surface from 50,000 BC up to present (Yunana et al., 2017). LMNN is the fifth or ninth largest freshwater lake in the world (by volume/surface area), and it is an example of a vital water resource for hydropower generation yet a vulnerable hydro-system in the tropics (Mtilatila et al., 2020). LMNN is a shared water resource between Malawi, Mozambique and Tanzania.

Lake Tanganyika is a meromictic lake, second largest lake (by area) in Africa located in East Africa with a maximum depth of 1,470 m, and the second oldest and deepest lake in the world (Verburg and Hecky, 2009; Naithani et al., 2011). It is a shared water resource between Burundi, the Democratic Republic of Congo (DRC), Tanzania and Zambia. The lake is surrounded by poor countries whose inhabitants strongly depend on this resource for their basic needs such as intensive fishery (Sterckx et al., 2023). Although Lake Tanganyika is undergoing significant changes because of the climate change, it is unknown how these changes may affect the lacustrine system’s ability to function in the future (Sterckx et al., 2023). Climate change is also affecting Lake Victoria, the biggest and second largest freshwater lake in Africa and earth, respectively. It is also an important source of livelihoods for more than 30 million people living in three riparian countries (Tanzania, Kenya and Uganda) and indirectly supports another 340 million people along the Nile Basin being the source of the White Nile (Awange et al., 2013).

This review was conducted in line with the PRISMA guidelines. The PRISMA framework ensures a methodical and repeatable approach to the identification, screening, eligibility evaluation, and extraction of data from literature (Odoi-Yorke, 2024). Peer reviewed journal articles published between 2000 and March 25, 2024, were extracted from the Scopus as main database and Google scholar as a top-up database for systematic review. Scopus was chosen as the primary database because it is a broad abstracting and indexing database that facilitates access to a wide range of international publications, guaranteeing comprehensive worldwide coverage of research findings from various geographic locations (Odoi-Yorke, 2024). Additionally, Web of Science papers are indexed in Scopus. Key words such as ‘lake names’, ‘climate change’, ‘climate variability’, ‘ECEs’ were used to extract relevant journal articles from the two databases (Table 1).

A generic and refined search from Scopus database was done and it yielded 866. This was followed by a refined search protocol that yielded 139 articles considered for manual abstract screening. Both search protocols are presented herein.

Table 2 further shows details on the exclusion and exclusion criteria that was used. Such criteria included issues like language and period.

No duplicate papers were found out of the 139 documents that were extracted from Scopus for abstract screening. Only 70 articles made it to the stage for full paper screening. A total of 69 articles abstracts from Scopus were successfully downloaded. Further screening of the 69 papers was done to exclude articles older than 2000 and a total of 14 papers were removed and 55 were eligible for full paper screening. After full paper screening, 6 articles were found to be irrelevant and 49 were selected for systematic literature review. Top-up articles from Google scholar were also extracted using the aforementioned key words and a total of 29 articles were extracted. Checking for duplicates on articles from Scopus versus Google data database was done and some duplicates were found and those from the former database were excluded, and 29 articles remained for review. A total of 78 articles were used for systematic literature review. Figure 2 shows the PRISMA flow chart from both the abstracts and full documents text screening.

Using ATLAS. Ti 24 software, data from the literature review was analysed. Themes and/or codes based on the climate parameters, lake parameters, hydrological and economic activity changes were noted. ‘Invivo’ coding was supplemented with emerging codes as some impacts were unique to certain lakes. Generation of quotations and codes was done at the same time. Coding was then followed by grouping the codes into code groups that became the themes for the study. The analysis initially focused on impacts associated with each lake followed by comparative analysis across all the lakes. Network and co-occurrence analysis of the codes was done and then across all lakes.

Climate change is first evident with a change in the climate parameters of an area. The interaction and/or individual effect of these climate parameters has disproportionate influences on the lakes, especially their size, lake level, nutrient and water mixing, water temperature and lake productivity. Climate change trigger ECEs that implicitly and explicitly affect lake basins. Figure 3 shows some notable ECEs (though they varied by lake) their interactions and how they were affecting the four lake basin ecosystems.

Climate change influence the trajectory of climate parameters, intensity and frequency of ECEs. Table 3 summarizes observed and projected changes in climate parameters and ECEs from Lake Chad and/or its basin. Temperature for Lake Chad Basin, the number and frequency of warm days are expected to increase in the future leading to a decline in cool night frequency, and diurnal temperature from 2016 to 2035.

The lake basin was expected to experience more, and stronger droughts from 2020 to 2040, compared to the 1970s. This will be interspersed with sporadic floods, especially on the lake beds where migrant fishermen from other places have seen an opportunity to build their homes. However, there are contradictory findings on the rainfall trajectory of the basin. There are reports that rainfall levels and extreme rainfall events have been increasing across the basin and the eastern Sahel region since 1990 (Bouchez et al., 2016; Pham-Duc et al., 2020; Daoust and Selby, 2023; Gbetkom et al., 2023). However, Nkiaka et al. (2017a) state that annual and seasonal precipitations reduced with moderate and strong downward trends for modeled and observed precipitation, respectively. This makes it difficult for water resources managers to sustainably manage water resources in the basin in the context of contradictory futureprojections.

Although there are contradictory future projections on the rainfall pattern for Lake Chad Basin, it is indisputable that temperatures and drought intensity are increasing thereby affecting lake’s physical, biological, and chemical parameters. Table 4 shows some climate change induced ecosystem changes and human activities. The 1965 to early 1970s droughts rapidly reduced lake levels and depth leading to the division of the once great lake into two pools and a dryland (Great Barrier) between them. Rainfall variability after the 1965 to 1970 droughts led to the separation of the southern and northern pools as the lake levels lowered (Fraedrich, 2015; Bouchez et al., 2016).

From Table 4 it emerges that the drying of lake-bed and the creation of the ‘Great Barrier’ led to vegetation colonization on dryland (Great Barrier) dividing the two pools. The establishment of permanent vegetation on the barrier is also contributing to increased infiltration and the reduction in runoff from the southern pool to the northern pool through the Great Barrier (Pham-Duc et al., 2020). Okonkwo et al. (2014) reported a negative correlation as witnessed by increasing precipitation in the Lake Chad Basin but decreasing river discharge and lake level. Climate change and human activities caused a 59 and 41% decline in streamflow between 1965 and 1972, respectively, while human activities dominated with 66% between 1973 and 2013 (Mahmood and Jia, 2019).

However, in from other publications, the decrease in lake levels during the 1980s and 1990s, has been attributed mainly to human activities such as land use changes in the basin, water withdrawals for irrigation (Mahmood and Jia, 2019). This implies that climate change just added an additional layer to an already existing problem. Warming of lakes and subsequent decline in lake depth has led to a decline in the quantity of fish in the lake. Warming results in water temperature thresholds being reached for certain species (Abdel-Fattah and Krantzberg, 2014). Since 2000, the lake surface area and water stored in the aquifer beneath the lake has increased due to more favorable rainfall in basin and the western Sahel (Bouchez et al., 2016) dispelling myths that the lake will get extinct in the near future. Fishermen had the greatest vulnerability to climate change compared to farmers and pastoralists due to low fish catches and measures put in place to promote climate resilient fisheries. Crop farmers and pastoralists reported losses in crops and decline in livestock product quality due to droughts and also floods for the former as some migrants had turned drying lake beds into arable land.

Table 5 shows that minimum, maximum atmospheric, and surface water temperatures have increased while daytime temperatures are becoming warmer and cold days decreasing. This might likely lead to the extension of the malaria belt into the highlands of Lake Victoria Basin. However, scholars such as Luhunga and Songoro (2020) project a non-significant decrease in rainfall, while Beverly et al. (2020), Khaki and Awange (2019), and Pietroiusti et al. (2024) state that future precipitation is uncertain. Shinhu et al. (2023) projects an increase in rainfall over the whole lake for the 2030–2060 period. The uncertainty is not peculiar to precipitation patterns only, but also the length of the growing season as projections point to an increase and reduction in rain season across the basin. There are also projected significant declines in wind speed, gustiness, strong waves assumed to be previously associated with heavy thunderstorms (Van de Walle et al., 2021). Although there is a decline in wind speed and intensity, sporadic cases of thunderstorm-induced strong waves capable of capsizing fisher boats, passenger ferries and goods transport boats are still a problem over the lake (Van de Walle et al., 2021; Table 5). Although the lake has been associated with ECEs such as droughts in the 1980s, future climate projections for the 2030–2060 period point to an increase in intense storms and subsequently flooding of the basin.

Table 6 shows that the dam and Basin has been characterized by significant variations in lake levels, with negative years due climate variability and anthropogenic activities such the expansion of Owen Falls dam and Nalubaale Dams in Uganda and between 2003 and 2007, stable period (2007–2011) and significant increase between 2007 and 2012, 2019–2020 leading to a general slight increase from 2003 and 2020 (Khaki and Awange, 2019; Beverly et al., 2020). Awange et al. (2019) argues that such positive trends dismiss the views by Beverly et al. (2020) of lake level reduction by the end of 21st century, and its disappearance in as little as 3,500 years.

The projected future inter-annual variations in rainfall are positively linked to projected inter-annual discharge variations for 8 out of 9 rivers feeding the Lake Victoria Basin from 2015 to 2100. Scholars also observed no major changes in primary production except an increase in algal blooms, which deplete dissolved oxygen when they die leading to deaths of fish in the lake. Such sporadic strong waves, intense storms and over-lake thunderstorms affect water-based activities including fishing as these may lead to boats capsizing (Thiery et al., 2016; Van de Walle et al., 2021; Nyamweya et al., 2023; Ogega et al., 2023). However, future projections in temperature show increased atmospheric and uncertain rainfall patterns, which will affect rain-fed crop and irrigation farming through water shortages and high rates of evapotranspiration.

River discharge is also projected to display inter-annual variations, which has the potential to affect the generation of hydro-electricity production in Sondu Miriu, Kagera rivers, and at the outlet of the Nile in Uganda, proposed projects on Gucha, Yala, and Nzoia rivers in Kenya (Olaka et al., 2019; Beverly et al., 2020) and other activities depend on water withdrawal in the region. However, the 2019–2020 rainfall figures show that lake outflow was insufficient to balance the increased input into the lake leading to flooding (Pietroiusti et al., 2024). Furthermore, projections of intense storms between 2030 and 2060, increasing floods up to 2,100 due to projected 10–20% increase in stream flows by 2040 with inter-annual variations, thereafter, point to future increase in lake levels (Thiery et al., 2016; Olaka et al., 2019; Van de Walle et al., 2021; Pietroiusti et al., 2024). This will increase hydro-electricity production in the future. While river discharge is expected to experience interannual variations, the increasing temperatures and lake evaporation in future will lead to lake shrinkage and exploitation of lake shores by the vegetation. According to Awange et al. (2019) vegetation cover and the normalized vegetation index (NDVI) calculations are showing an upward trend around the LV shores experiencing shrinkage.

The LMNNB has experienced atmospheric warming with the 1990–2000 decade being regarded as the warmest as witnessed by significant increases in temperatures and evaporation. The basin is facing a negative correlation characterized by the fall in annual rainfall and increase in the frequency of droughts (Table 7). Besides droughts, LMNN is prone to the ECE, the strong easterly winds, commonly known as the ‘Mwera’ winds. These Mwera winds result in internal lake seiches and/or strong waves that drive water-nutrient upwelling and horizontal density disequilibrium in the lake (Limuwa et al., 2018; Banda et al., 2020). The strength of the Mwera winds and resultant lake seiches are due to obstruction-free nature of the lake surface, which causes the rapid deterioration in the lake condition and flooding (Limuwa et al., 2018). The ‘Mwera’ winds also lead to upwelling in the southern part of the lake which is a favorable condition for vertical water exchange and introduction of nutrient-rich deeper water into surface waters (Chavula et al., 2023).

Table 8 shows that there has been a decrease in annual precipitation, an increase in temperature and the occurrence of more severe droughts in LMNNB. These phenomena are expected to lead to a decrease in the mean lake levels both in the near and far future. Mtilatila et al. (2020) state that the influence of precipitation on lake level changes is slightly larger than the effect on temperature on LMNN. The lake crossed the Lake Malawi Outflow Threshold (LMOT) in the early 20th century, thereby sealing the LMNNB and halting the outflow into the Shire River (Bhave et al., 2020; Ngongondo et al., 2020). The current and projections of increasing temperature and decreasing precipitation for the 2021–2050 and 2071–2100 periods will lead to a significant decrease in Rufiji and Shire River discharge which are important for hydropower productivity (Mtilatila et al., 2020; Siderius et al., 2021). The decline in precipitation and increase in temperatures provide favorable conditions for the growth of algal blooms that consume oxygen when they die. This has been linked to changes in primary production, fish species amount, composition and sizes as compared to last 20 years (Chavula et al., 2023). However, the increasing strength of the Mwera winds’ is contributing to upwelling of nutrient rich deep waters enhances phytoplankton production and sustains fish production in the only southern part of lake.

Limuwa et al. (2018) report that extreme and frequent occurrences of Mwera winds induced seiches mades fishing using boats too risky. This has been worsened by the decline in Chambo fish since 20,005 due to population pressure, consumption of oxygen at the death of algal blooms declining rainfall in the lake (Makwinja and M. M’balaka., 2017). Invasive species are also colonizing the shrinking lake-bed. Changes in climate of the lake basin will further affect economic activities like hydropower generation and crop farming as they are depended on rainfall and accumulated runoff in the lake.

From Table 9, it emerges that atmospheric warming has been evidenced through the significant warming of the surface of Lake Tanganyika over the last century average at a rate of 0.129 from 1912 to 2013 (Kraemer et al., 2015; Phiri et al., 2023). Lake surface warming is expected to worsen as forecasts indicate that air temperature will increase by 1°C to 3°C between 2010 and 2050 (Plisnier et al., 2018). The increase in temperature has been coupled with unpredictable rainfall, short rain season (Kraemer et al., 2015; Bulengela et al., 2020; Phiri et al., 2023) and decline in wind speed by about 30% since the late 1970s over the lake and lake basin (Plisnier et al., 2018). Despite a decline in wind speed, Naithani et al. (2011) state that Lake Tanganyika is still prone sporadic strong winds, which cause lake surface seiches (Chimbanfula waves) and subsequent flooding of lake coastal areas (lake ‘throwing up’), wetlands and Ruzizi Delta Nature Reserve, for instance in 2019–2020 (Gbetkom et al., 2024).

Table 10 shows that lake level experienced a downward trend between 2003 and 2006, followed by a positive trend from 2007 up to present. The wind speeds across the lake declined leading to lake surface warming as there was reduced mixing of shallower and deeper waters to dilute the surface water temperature. However, Kevin Sterckx et al. (2023) argue that lower wind speed and the resultant high surface water temperature were not induced by climate change, but these are associated with the northern part of Lake Tanganyika. This side is surrounded by mountains, while the southern part of the lake has greater surface cooling and deeper mixing due to the effect of the strong southerly winds during the cool season. However, some scholars (Plisnier et al., 2018; Sayers et al., 2020) argue that the whole lake experienced decline in wind speeds that reduced mixing of nutrient rich deep and nutrient deficient surface waters. This is affecting primary production and fish abundance in the lake in even in seasons previously known to be of “good catch (Karasaji). However, the decline in sardine catches since the mid-20th century can be attributed solely to climate warming as the early phase of commercial fishing certainly aggravated the climate induced problem (Cohen et al., 2016).

An increase in temperature over the period 2010–2050 will not only affect also affect the fishing industry but lead to agricultural and biodiversity losses while at the same time indigenous species on drying lake shores will be replaced by invasive species (Plisnier et al., 2018).

Figure 4 shows the connection between climate parameters, ECEs and related changes in lake ecosystems across the four lake basins. Rainfall and temperature change are the main climate parameters contributing to changes in lake ecosystems, water, and non-water-based human activities. Out of all the ECEs, droughts, strong winds and floods dominate in terms of their impacts on lake-based ecosystems. The change in climate parameters such as rainfall, temperature and increase in droughts and flooding mainly affect lake activities and ecosystems such as fishing, lake level, aquatic life and nutrient/water mixing across all the lakes. Fishing activities and lake levels are affected by changes in almost all the climate parameters and an increase in the frequency and intensity of ECEs. Rainfall change is the dominant climate change component mainly linked to changes in lake levels, river discharge and economic activities such as fishing and hydro power generation.

While lakes and their basins are all prone to climate change and ECEs, the observed and projected nature, intensity, and frequency of these ECEs vary from lake to lake. In terms of reported cases of ECEs, the Lake Victoria Basin had the highest (6) followed by LMNN, Lake Tanganyika and lastly Lake Chad (Figure 5). However, the highest number of ECEs reported does not translate into the highest frequency and intensity of the ECEs and lake ecosystems high vulnerability. Floods are a common ECE across all four lakes though their causes vary from lake to Lake. Floods in Lake Victoria are caused by intense storms and of late they were triggered by thunderstorm-induced waves. In Lake Malawi and Lake Tanganyika, floods are by strong winds (Mwera winds in Malawi) that result in internal lake seiches or strong waves (Chimbanfula waves in Tanganyika) causing the rapid deterioration in the lake ‘throwing up’ and flooding. However, reports of floods in Lake Chad are associated with flooding of drying lake beds where migrant fishers established farmlands and homesteads. Floods have also been linked with increasing cases of extreme rainfall events over Lake Chad Basin since the 1990s. Drought is also common in all the lakes except for Lake Tanganyika Basin despite temperature increase, lake surface warming of 0.129°C over the last century and decreasing lake levels between 2003 and 2006. The droughts and Mwera winds were the main reported ECES affecting LMNN, drought for Lake Chad Basin, flooding for Lake Victoria Basin and Lake Tanganyika Basin.

Climate change and increased incidence of ECEs lead to different impacts on lake-based ecosystems. While water levels for Lake Chad and Lake Tanganyika are rising, Lake Victoria’s level is stable, and LMNN is experiencing a decline. The decline in lake levels has exposed dryland in the lakes leading to human occupation and vegetation colonization. The drying lake shores for Lake Chad and Lake Victoria are being colonized by indigenous vegetation, but those from Lake Tanganyika and LMNN are being colonized by invasive species. Such invasive species have a greater affinity for water leading to high evapotranspiration. The decline in the lake level for LMNN has led to the exposure of a sand bar at the lake outlet and seasonal river discharge in the Shire River. Changes in wind conditions, temperature and rainfall have also led to a decline in fish quantity except for the southern part of LMNN where there is an increase in plankton.