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Indices of abundance are usually a key input parameter used for fitting a stock assessment model, as they provide abundance estimates representative of the fraction of the stock that is vulnerable to fishing. These indices can be estimated from catches derived from fishery-dependent sources, such as catch per unit effort (CPUE) and landings per unit effort (LPUE), or from scientific survey data (e.g., relative population number—RPN). However, fluctuations in many factors (e.g., vessel size, period, area, gear) may affect the catch rates, bringing the need to evaluate the appropriateness of the statistical models for the standardization process. In this research, we analyzed different generalized linear models to select the best technique to standardize catch rates of target and non-target species from fishery dependent (CPUE and LPUE) and independent (RPN) data. The examined error distribution models were gamma, lognormal, tweedie, and hurdle models. For hurdle, positive observations were analyzed assuming a lognormal (hurdle–lognormal) or gamma (hurdle–gamma) error distribution. Based on deviance table analyses and diagnostic checks, the hurdle–lognormal was the statistical model that best satisfied the underlying characteristics of the different data sets. Finally, catch rates (CPUE, LPUE and RPN) of the thornback ray Raja clavata, blackbelly rosefish Helicolenus dactylopterus, and common mora Mora moro from the NE Atlantic (Azores region) were standardized. The analyses confirmed the spatial and temporal nature of their distribution.