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This study reports the comparative studies and microbial risk assessment of different water samples used for processing frozen sea-foods in Ijora-olopa, Lagos State, Nigeria. Twelve different samples of well, tap, borne-hole, river water used for processing frozen sea-foods were collected from different processing shops in Ijora-olopa, Lagos. These water samples were microbiologically analyzed for the presence of microorganisms. Total plate counts and total coliform counts were enumerated using Plate Count Agar (PCA) and Eosin Methylene Blue (EMB) Agar, respectively. The total count of most the water samples ranges between 0.48 x 102 and 2.04 x 102 CFU/ml, exceeding the limit of 1.0 x 102 CFU/ml. The coliform counts per 100 ml of water samples ranged between 15 and 184 cells. Fifteen (15) isolates were characterized from the samples on PCA with percentage of occurrence of different microorganisms characterized as follows: Bacillus cereus (33.3%), Enterobacter aerogenes (33.3%), Flavobacterium sp. (13.3%), Micrococcus sp. (6.7%), Pseudomonasaerugionosa (6.7%) and Staphylococcus auerus (6.7%). Some of these organisms are of public health significance. Studies show the possibilities of survival of pathogenic microorganisms during water treatment/seafood processing. Therefore, stringent quality assurance measures should be put in order to safe guard the health of the consumers