Transitional ecosystems, estuaries and the coastal seas, are distinctively affected by natural and anthropogenic factors. Organic matter (OM) originating from terrestrial sources is exported by rivers and forms a key component of the global biogeochemical cycles. Most previous studies focused on the bulk biochemical and anthropogenic aspects affecting these ecosystems. In the present study, we examined the sources and fate of OM entrained within suspended particulate matter (SPM) of the Zuari River and its estuary, west coast of India. Besides using amino acid (AA) enantiomers (L- and D-forms) as biomarkers, other bulk biochemical parameters viz. particulate organic carbon (POC), δ13C, particulate nitrogen (PN), δ15N and chlorophyll a were analyzed. Surprisingly no significant temporal variations were observed in the parameters analyzed; nonetheless, salinity, POC, δ13C, PN,δ15N, glutamic acid, serine, alanine, tyrosine, leucine and D-aspartic acid exhibited significant spatial variability suggesting source differentiation. The POC content displayed weak temporal variability with low values observed during the post-monsoon season attributed to inputs from mixed sources. Estuarine samples were less depleted than the riverine samples suggesting contributions from marine plankton in addition to contributions from river plankton and terrestrial C3 plants detritus. Labile OM was observed during the monsoon and post-monsoonseasons in the estuarine region. More degraded OM was noticed during the pre-monsoon season. Principal component analysis was used to ascertain the sources and factors influencing OM. Principally five factors were extracted explaining 84.52％ of the total variance. The first component accounted for 27.10％ of the variance suggesting the dominance of tidal influence whereas, the second component accounted for heterotrophic bacteria and their remnants associated with the particulate matter, contributing primarily to the AA pool. Based on this study we ascertained the role of the estuarine turbidity maximum (ETM) controlling the sources of POM and its implications to small tropical rivers. Thus, changes in temporal and regional settings are more likely to affect the natural biogeochemical cycles of small tropical rivers.