The levels of heavy metals were determined in environmental samples; water, flora and sediments along the Thika River, specifically, to investigate their distribution and to determine the extent of pollution. Water, sediment and algae (Cladophora) samples were each collected from thirty-two (32) sampling sites identified along the river’s profile and each analyzed for the selected heavy metal content using TXRF and EDXRF. In general, the concentration levels of heavy metals in water samples ( gl-1) were determined as follows; Mn (53.5 -605), Cu (< 10 -303), Zn (22-325), Ni(< 15 - 77), Pb (< 10 -84) while those in sediment samples (mg kg-1) were; Mn (2230-8659), Cu (51 -115), Zn (153-432), Ni (67 - 172), Pb (32-177). The results of the concentration levels of heavy metals in Cladophora (mg kg- 1) ranged as follows; Mn (3719 - 21200), Cu (65-129), Zn (153-434), Ni (35 -235), Pb (17 - 72). There was a significant difference in heavy metal concentrations between the three media for all elements studied. Based on results of enrichment factors, geoaccumulation indices, pollution load index (PLI), contamination factors and modified degree of contamination, all sampled sediments were generally contaminated with, Cu, Zn, Mn and Ni to a moderate degree, hence requires intervention to curb on the rising levels of pollutants. Statistically significant interrelationship was observed between sediments and Cladophora, which supports the idea that, Cladophora is an appropriate bio-indicator for heavy metal pollution. Heavy metal contamination levels in water samples, in this study, is variously impacted by; nearby industries, dust from the nearby mining activities and the chemical fertilizers used in the nearby commercial pineapple farms and combustion of fuel from the vehicles plying the nearby roads and therefore unsuitable for drinking. The study consequently, recommends for the introduction of heavy metal bio-accumulators such as bamboo plants grown along Thika River basin and for enforcement of measures to restrict direct release of untreated waste waters and industrial effluents, into the river. Further studies should also be carried out to determine the other sources contributing to the pollution of the river ecosystem.