Lake Maninjau, like many surface water bodies worldwide, faces significant water pollution challenges due to extensive aquaculture activities, making it an ideal site to study the impact of fish farming on water quality, which has contributed to eutrophication and declining water quality. This study investigates the physicochemical parameters and pollution levels in the lake, aiming to provide insights into its environmental health. In August 2022, a comprehensive sampling campaign was undertaken at nine stations within the upper layers of open water and littoral zones of Lake Maninjau. In situ measurements, including temperature, dissolved oxygen, and pH, were conducted, accompanied by water sample collection for laboratory analysis of trace elements and heavy metals. Our study revealed notable variability in water parameters across different sites, with surface water layers exhibiting the greatest differences. While certain parameters such as temperature and conductivity remain relatively stable, pH levels show a decreasing trend with increasing water depth. Dissolved oxygen levels vary widely, while oxidation–reduction potential indicates water pollution, particularly in littoral zones. Potassium dominance within cations likely suggests anthropogenic influences, notably from aquaculture activities, that may also contribute to nutrient enrichment and heavy metal pollution. Elevated levels of total nitrogen and ammonia underscore the lake’s moderate pollution levels, with heavy metals such as mercury exceeding permissible limits, posing risks to aquatic life and human health.