The impact of removal of riparian vegetations on primary productivity of the Otamiri River in the Federal University of Technology, Owerri, Nigeria was investigated in early 2013. Two sampling locations (OL 1 & OL 2) sited at vegetated segments and 3 others (OL 3, OL 4 and OL 5) sited about 50m apart within a de-vegetated segment of the river were studied. The light and dark bottle technique was used for the estimation of primary productivity and in situ measurements made with the HANNA HI 9828 pH/ORP/EC/DO meter for pH, water temperature, electrical conductivity, total dissolved solids (TDS) and salinity. Other parameters were determined using standard methods. The descriptive statistics, single factor ANOVA, means plots, student’s t-test, Pearson correlation (r) and linear regression were used to analyse data. Maximum gross (2.82mgCL-1d -1) and net primary productivity (2.52mgCL-1d -1) (GPP & NPP) as well community respiration (CR) (0.30mgCL-1d -1) were all recorded in the non-de-vegetated OL 2 while highest temperatures (28.34 ± 0.269 °C) were recorded in the de-vegetated segments of the river. There was marked heterogeneity in yields of productivity across the sampling locations [F(17.63)>Fcrit(4.20)], and GPP contributed the difference most at P<0.05. Temperature, with insignificant spatial correlationship (Sig, r=0.953) however differed markedly between the vegetated and de-vegetated locations (Sig. t=0.023) at P<0.05. Temperature also exerted very significant limiting influence on GPP (r=-0.961) and NPP (r=- 0.971) at P<0.01, even as the linear regression model revealed that a unit increase in temperature regime of the devegetated segment of the river would result in about 48.899 times decrease of yields in GPP. Results underpin the importance of riparian covers in watershed management of a tropical river system.