A novel integrated process for the recovery of protein-enriched biomasses from shrimp boiling water (SBW) and shrimp peeling water (SPW) was investigated by combining flocculation (F) and dissolved air flotation (DAF) into an F-DAF process. Alginate and carrageenan were used as flocculants. It was found that the protein yield from SPW and SBW in the F-DAF process was 68−97% and 26− 45%, respectively. This led to a reduction in protein content of the influent SBW and SPW (12.4 and 1.4 g/L, respectively) by up to 76% and 85%, resulting in outlets with 2.9 and 0.2 g/L protein, respectively. Further, the F-DAF recovery process concentrated the proteins of SBW and SPW up to 7 and 29 times, respectively, thus, generating a protein-enriched biomass. After spray drying, biomass from SBW had up to 61% proteins, and out of the total amino acids, up to 47% were essential ones. Further, the spray dried powder contained up to 23% total lipids, 2.7% long chained n-3 polyunsaturated fatty acids and 49.7 mg/g total astaxanthin. The studied F-DAF recovery system can thus be successfully used for recovering nutrients from process waters generated during the production of peeled shrimps.