In the past, experimental fishing with square mesh codends was conducted with the expectation that this would lead to a better defined size selection indicated by a smaller selection range (SR) of haddock (Melanogrammus aeglefinus) and other gadoid species compared to that provided by traditional diamond mesh codends. However, experimental results demonstrated considerable between-haul variations in the selection parameters (L50 and SR). It was speculated that these results could be linked to differences in morphology of individual haddock of the same length. In the present study we assessed which measures of haddock morphology are important for size selection through meshes. We quantified between-individual variation in morphology and used simulation techniques to estimate that this variation can account for less than 28% (range 15–28%) of the SR values found during experimental fishing. By including a realistic range of mesh openings when simulating the fishing process of a square mesh codend, we were able to explain most of the experimental results. Additionally, we used our method to better understand the seasonal variation in size selectivity reported in the literature and to predict the basic selective properties for haddock for other mesh shapes. Finally, we found that the conditions of our model, which describes mesh penetration for haddock based on assessment of morphology, is very similar to the conditions previously applied in the literature to study size selection of haddock in diamond mesh codends.