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In this study, we evaluated the sensing performance of silver nanoprism/graphene oxide/silicon nanowires (AgNPr/GO/SiNWs) nanohybrid system for effective detection of organic dye and herbicide residues in freshwater via surface-enhanced Raman scattering (SERS). Homogenous and vertically aligned SiNWs have been successfully synthesized using metal-assisted chemical etching technique by varying the etching time from 10 to 30 min. AgNPr/GO/SiNW hybrids were assembled by spin-coating of GO followed by drop-casting deposition of AgNPr. The microstructures of AgNPr/GO/SiNWs are strongly affected by the etching time of SiNWs, which in turn affected its SERS performance when rhodamine 6G is used as an analyte molecule. Owing to the synergetic effects of GO and AgNPr, SERS response of AgNPr/GO/SiNWs composites were found to be superior compared to AgNPr/SiNWs. High efficiency of 6.1 x 1010 has been achieved with AgNPr/GO/SiNWs based sensor fabricated with 30-min etched SiNWs for rhodamine 6G. An effective way of rapid detection of drinking water pollutants such as methylene blue and atrazine up to picomolar (10-12 M) concentrations was demonstrated using these low-cost AgNPr/GO/SiNWs nanohybrids SERS sensors.