Lake Chilwa is shared by Malawi and Mozambique, it supports an important fishery and its watershed is undergoing rapid population growth and increasing utilization for agricultural production. It is a shallow, closed basin lake with extensive surrounding wetlands; and it has suffered several desiccation events in the last century. To better understand the current condition of the lake, we monitored a suite of physical, chemical and biological parameters at approximately monthly intervals over an annual cycle in 2004–2005. The limnology of the lake was extremely sensitive to seasonal changes in the lake's seasonal hydrological cycle. The physico-chemical parameters, temperature, electrical conductivity, and total suspended solids exhibited clear seasonal patterns driven by the highly seasonal rainfall and resultant lake levels. In response, phytoplankton and zooplankton abundance, as well as biologically dependent oxygen concentrations and pH, exhibited several maxima levels over the year. The peaks of phytoplankton and zooplankton were out of phase suggesting a lag in the zooplankton grazing in response to pulses in primary productivity. Chlorophyll concentrations can exceed 1 mg/L in surface waters indicative of hypereutrophic conditions, but they fell dramatically during zooplankton peaks. This hydrologically driven, shallow and mesohaline lake is a productive and critical resource to the region. Its management poses challenges arising from the dependence of its limnology and fishery on the lakes hydrology, catchment land use and climate variability.