Shrimp boiling water (SBW) and shrimp peeling water (SPW), generated during shrimp processing, were characterized in terms of crude composition, volatile compounds, as well as nutritional and potentially toxic elements over a 13 month sampling period. The storage stability of both waters was also evaluated. Results showed that SBW contained on median 14.8 g/L protein and 2.2 g/L total fatty acids with up to 50% comprising eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Astaxanthin esters, which dominated the total astaxanthin, were 2.8 mg/L on median. SPW, on the other hand, contained on median 1.0 g/L of protein, 0.21 g/L of total fatty acids, and 1.2 mg/L astaxanthin esters. For both side-streams, essential amino acids were up to 50% of total amino acids. For SBW and SPW, the most abundant nutritional elements were Na, K, P, Ca, Cu, and Zn. The contents of all potentially toxic elements were below the detection limits, except for As. SBW was more stable at 4 °C compared to SPW as shown, e.g., by thiobarbituric acid reactive substances and relative changes in total volatile basic nitrogen. The extensive compositional mapping of SBW/SPW provides crucial knowledge necessary in the exploitation and value-adding of such side-streams into food or feed products.