Water Framework Directive (WFD) guidance documents from 2019 provide a comprehensive review of methods and guidelines to improve the comparability of heavily modified water bodies (HMWBs) in the European Union. However, there is currently no common, single methodology for monitoring HMWBs and artificial water bodies (AWBs) or for determining maximum (MEP) and good ecological potential (GEP). This study presents the first assessment of hydromorphological conditions of HMWBs and AWBs in Croatia based on type-specific indicators. The typology of HMWBs and AWBs was based on distinct hydromorphological characteristics and modifications in order to be easily related to the uses of the water bodies. The classes of hydromorphological potential were graded from the theoretical MEP, which was determined by the score scale as the tolerated deviation from natural reference conditions, considering potential mitigation measures. The use of the water body and/or the effects on the wider environment were considered while determining MEP and choosing indicators included in monitoring and assessment. In the case of AWBs, the parameters dependent on natural reference conditions, which are non-existent, were omitted from the assessment. Only 27% of HMWBs and 2 out of 51 AWBs achieved good potential for all three hydromorphological elements. The most significant hydromorphological modifications include channelization, straightening, deepening and removal of riparian vegetation due to flood-protection management practices. In order to achieve the environmental objectives set out by the WFD, the Croatian water management system has to start implementing mitigation measures, especially related to natural flood management.