The implementation of protected areas, in particular, nature Conservation Units (CUs), is a conservation strategy recognised worldwide. However, these territories require efficient management to achieve their conservation goals. When the management of CUs is deficient, it results in damage to their own goals, affecting biodiversity and ecological processes, as well as causing social and economic impacts. In this context, we evaluated the management effectiveness of 11 integral Conservation Units of nature in the State of Rio Grande do Sul, southern Brazil, through interviews, visits to these CUs and a review of their official documents. For this analysis, we used the adapted method of Effectiveness of Management of Protected Areas (EMAP), which was analysed using a Likert scale with five levels, eight scopes, 73 indicators and 65 evaluation scenarios. Ninety-one percent of the CUs assessed in southern Brazil by the EMAP method oscillated from average to very unsatisfactory efficacy and low management effectiveness: 18% of the CUs had a very unsatisfactory quality of management, 37% unsatisfactory, 36% average and only 9% high or satisfactory. Moreover, the CUs did not fulfil the main objectives for which they were created. In this context, we recommended a series of actions to be applied for CU improvement, such as the adoption of a quali-quantitative evaluation model for the units, through a mathematical model; increase in staff; training teams and managers; improvement of CU infrastructure and inputs; regular budget allocation; land regularisation, implementation of consultative councils and urgent review of management plans.