The presence of two morphotypes of Arctic charr Salvelinus alpinus was confirmed via morphological variation and otolith strontium (Sr) within three open‐lake systems of southern Baffin Island, Nunavut, Canada: Qinngu (LH001), Iqalugaarjuit Lake (PG082) and Qasigiat (PG015). Analysis of otolith Sr indicates that a component of each S. alpinus population within lakes LH001 and PG082 is migratory (large–maturing S. alpinus), whereas another component is lake‐resident (small–maturing S. alpinus). Alternatively, small and large maturing S. alpinus may both inhabit tidal habitats during their lifetime in lake PG015. Three morphological characters were identified by principal factor analysis (PFA) as characters that were different between maturity groups for all lakes studied: eye diameter, pectoral fin length and pelvic fin length. As well, upper jaw length (LH001 and PG082) and fork depth (PG015) were identified in PFA as traits that differed between morphs. Univariate tests of morphological characters identified by PFA demonstrated maturity group differences with the exception of eye diameter in Lake PG015 and upper jaw length and pelvic fin length in lake LH001. No difference was found in the MANOVA test of upper and lower gill raker number between small–maturing and undeveloped fish within all lakes studied. Clear morphological variation observed between small–maturing and undeveloped fish in all three lakes of the study suggests ecological niche separation between morphotypes. This is the first documented case of lake‐resident S. alpinus use of the tidal habitat in the presence of a migratory large–maturing morphotype.