The present study focllses 011 the IiI1l11ogeological aspects of the lakes Sagara and Nyalllagoma within tITe Malagarasi Wetland Ecosystem. Abiotic parameters frol11 water and sediment samples were determined during the d,y and wet seasons using appropriate gears and methods. The data show variation of the abiotic parameters in both lakes from the water sUiface to the bottolll. Lake Nyamagoma is less turbid (0.7-24 NTU) than Lake Sagara (25 to 65 NTU). The water transparency was also high at Lake Nyamagollla (0.75-1.5 111) thus supporting the observed turbidity trend. The physical chemical changes may be attributed to processes such as cooling, dissociation, dissolutioll, decomposition, adsorption, precipitation, cation exchange and photosynthesis. However, higher nutrient concentration was obsel1Jed in the wet season than d,y season with the exception of SiD] consequent to dilution effect by sUlface runoff. The mineralogical content (Kaolinite, Smectite, lllite and Quartz) of the lake sediments indicate existence of good drainage conditions at the lakes as supported by the geology of the area, It is recommended that a long-term lilllnogeological mOllitoring alld evaluation be conducted so as to understand future nutrient hydrodynamics and hydrological functioning of the wetland ecosystem.