Over-exploitation of tropical lakes and reservoirs (‘lakes’) causes water quality problems that occur as a result of competing socio-economic demands and the presence of feedback loops within the system that exacerbate the situation. We review well documented case studies from Brazil, India, Indonesia, Kenya, Malaysia and Mexico to examine the effect that changes in water quality and quantity have had on the utilisation of these tropical lakes. By comparing the different approaches used to improve their sustainable management, we have found that nutrient enrichment is one of the most important and widespread water quality problems, causing adverse effects such as algal blooms, nuisance levels of aquatic plants, low oxygen levels and elevated greenhouse gas emissions. These effects restrict the use of these lakes for water supply, fisheries, recreation, tourism and wildlife. We conclude that tropical lakes require better management, urgently, to restore the ecosystem services that they deliver to man and nature. However, to be effective, the development of sustainable management programmes needs to be underpinned by reliable scientific evidence and the results of extensive stakeholder engagement activities. We note that, currently, there is little information available on how tropical lakes respond to management interventions that can be used to guide these activities. Further research is needed to address this knowledge gap.

In freshwater systems, cyanobacteria are strong competitors under enhanced temperature and eutrophic conditions. Understanding their adaptive and evolutionary potential to multiple environmental states allows us to accurately predict their response to future conditions. To better understand if the combined impacts of temperature and nutrient limitation could suppress the cyanobacterial blooms, a single strain of Microcystis aeruginosa was inoculated into natural phytoplankton communities with different nutrient conditions: oligotrophic, eutrophic and eutrophic with the addition of bentophos. We found that the use of the bentophos treatment causes significant differences in prokaryotic and eukaryotic communities. This resulted in reduced biodiversity among the eukaryotes and a decline in cyanobacterial abundance suggesting phosphorus limitation had a strong impact on the community structure. The low temperature during the experiment lead to the disappearance of M. aeruginosa in all treatments and gave other phytoplankton groups a competitive advantage leading to the dominance of the eukaryotic families that have diverse morphologies and nutritional modes. These results show cyanobacteria have a reduced competitive advantage under certain temperature and nutrient limiting conditions and therefore, controlling phosphorus concentrations could be a possible mitigation strategy for managing harmful cyanobacterial blooms in a future warmer climate.

Rapid development and climate change in southeast Asia is placing unprecedented pressures on freshwater ecosystems, but long term records of the ecological consequences are rare. Here we examine one basin of Tasik Chini (Malaysia), a UNESCO‐designated flood pulse wetland, where human disturbances (dam installation, iron ore mining, oil palm and rubber cultivation) have escalated since the 1980s. Diatom analysis and organic matter geochemistry (δ13Corg and C/N ratios) were applied to a sediment sequence to infer ecological changes in the basin since c. 1900 CE. As the Tasik Chini wetland is a rare ecosystem with an unknown diatom ecology, contemporary diatom habitats (plant surfaces, mud surfaces, rocks, plankton) were sampled from across the lake to help interpret the sedimentary record. Habitat specificity of diatoms was not strongly defined and, although planktonic and benthic groupings were distinctive, there was no difference in assemblages among the benthic habitat surfaces. An increase in the proportion of benthic diatom taxa suggests that a substantial decrease in water level occurred between c. 1938 and 1995 CE, initiated by a decline in rainfall (supported by regional meteorological data), which increased the hydrological isolation of the sub‐basin. Changes in the diatom assemblages were most marked after 1995 CE when the Chini dam was installed. After this time both δ13Corg and C/N decreased, suggesting an increase in autochthonous production relative to allochthonous river flood pulse inputs. Oil palm plantations and mining continued to expand after c. 1995 CE and we speculate that inputs of pollutants from these activities may have contributed to the marked ecological change. Together, our work shows that this sub‐basin of Tasik Chini has been particularly sensitive to, and impacted by, a combination of human and climatically induced changes due to its hydrologically isolated position.

Understanding how lakes respond to changes in nutrient loading along a productivity gradient can help identify key drivers of aquatic change, thereby allowing appropriate mitigation strategies to be developed. Physical, chemical and biological water column measurements combined with long-term water monitoring data for six closely located crater lakes, in Southeast Asia, were compared to assess the response of lakes along a productivity gradient equating to a transect of increasing aquaculture intensity. Increasing chlorophyll a (phytoplankton biomass) in the upper waters appeared to modify the thermocline depth and light availability causing a shift from a deep chlorophyll maximum at low aquaculture intensity to the emergence of algal dead zones lower in the water column with high aquaculture intensity. High phosphorus loading and light limitation from enhanced algal biomass, associated with high aquaculture intensity, exacerbated nitrogen drawdown, leading to the prevalence of potentially nitrogen-fixing cyanobacteria. Seasonal overturn during the cooler season resulted in low dissolved oxygen concentrations in the epilimnion, potential harmful algal blooms, a reduction in the habitable depth for fish and ultimately increased mortality amongst farmed fish.