We assessed protected area management effectiveness and identified attributes that limit the effectiveness of 21 protected areas in the State of Santa Catarina, southern Brazil. Of these, we assessed 10 areas under state-level administration for which a standardised assessment had not previously been conducted. For the 11 protected areas under federal administration, we obtained assessment data from the government. The protected areas were contrasted regarding the administration level and a list of attributes that could result in differences in management effectiveness between areas. We examined the relationship between protected areas' attributes and mean effectiveness using linear models. The same attributes were also related to management elements, namely context, planning, inputs, processes and outputs, using redundancy analysis. Management effectiveness and scores of management elements were found to be lower for areas either with unresolved land tenure, lacking management plans or updated ones, those under many pressures and threats, or those under state-level administration. Overall, we suggest that federal protected areas do better in at least these attributes or a combination of attributes not well-captured by single indicators than state-level protected areas. Reassessments should be regularly carried out across administration levels in order to effectively flag a barrier, clear it, and identify the next one to be tackled.