The surface stabilizing agents often play a major role in determining colloidal stability of the nanoparticles. In the present study a difference in surface coverage of colloidal silver nanoparticles was deliberately introduced by following two soft synthesis approaches: (a) biological process: using aqueous extract of Citrus limon [partial citrate capping] and (b) chemical process: using tri sodium citrate [complete capping]. Their aggregation behaviour in aqueous environmental matrix (lake water, sea water) and biological matrix (Potato Dextrose broth, Luria Bertani broth) was studied through UV-vis spectroscopy, hydrodynamic diameter, zeta potential analyses and theoretical studies (determining agglomeration number). Increase in ionic strength led to increased aggregation of the chemically synthesized nanoparticle whereas an exactly opposite result (decreased particle size in the presence of ions) was obtained for biologically synthesized one. The partially citrate coated nanoparticles [biological synthesis] exhibited significantly more colloidal stability in all the matrices studied compared to chemically synthesized particles. This study demonstrates that complete surface characterization of citrate capped silver nanoparticles is of high importance to understand its aggregation behaviour in aqueous matrices. © 2011 Elsevier B.V.