Restoration of the ecosystem services and functions of lakes requires an understanding of the turbidity dynamics in order to arrive at informed environmental management decisions. The understanding of the spatio-temporal dynamics of turbidity requires frequent monitoring of the turbidity components such as chlorophyll-a concentration. In this study, we explored the use of Moderate Resolution Imaging Spectroradiometer Aqua (MODIS-Aqua) satellite data in studying the spatio-temporal changes in chlorophyll-a concentration in Lake Naivasha, a turbid tropical system. The temporal trend of chlorophyll-a concentration over the study period in the lake was also evaluated. The temporal trend assessment was achieved through the removal of periodic seasonal interference using Seasonal-Trend decomposition based on the LOESS (Local Regression) procedure. The resultant chlorophyll-a concentration maps derived from MODIS-Aqua satellite data give an indication of the monthly spatial variation in chlorophyll-a concentration from 2002 to 2012. The results of regression analyses between satellite-derived chlorophyll-a and in situ measurements reveal a high level of precision, but with a measureable bias with the satellite underestimating actual in situ measurements (R2 = 0.65, P < 0.001). Although the actual values of the chlorophyll-a concentrations are underestimated, the significant relationship between satellite-derived chlorophyll-a and in situ measurements provides reliable information for studying spatial variations and temporal trends. In 2009 and 2010, it was difficult to detect chlorophyll-a from the MODIS-Aqua imagery, and this coincided with a period of the lowest water levels in Lake Naivasha. An inverse relationship between de-seasoned water level and chlorophyll-a concentration was evident. This study shows that MODIS-Aqua satellite data provide useful information on the spatio-temporal variations in Lake Naivasha, which is useful in establishing general trends that are more difficult to determine through routine ground measurements.