It is important to note that though appropriate assessment (Habitat Directive),and environmental impact assessment (EIA Directive)and strategic environmental assessment (SEA Directive) are similar in structure and have many connections they are still two distinctly different procedures. with different objectives . Although there are clear parallels between AA, SEA and EIA since all three are processes for assessing and minimising the environmental and sustainability impacts of plans and projects AA can not replace any portion of the standard EIA and standard EIA/SEA can not replace AA.

Appropriate assessment does not deal with impacts on all elements of biological and landscape diversity or conservation areas which have to be elaborated in appropriate chapters of EIA and SEA. Even the obligatory EIS /SEA chapter on biodiversity is much wider in scope (all habitats and species in the study area) than AA which analyses only impacts on species and habitats that are listed as sites' target features and impacts on overall site integrity. However, AA has to perform this analysis very thoroughly (precautionary principle) and give clear answer if plan or project is acceptable or not, (in other words if the negative impact on NATURA 2000 remains or not).

Results of the appropriate assessment are binding so in the case of negative conclusion project has to be rejected This is in stark contrast to SEA and EIA which does not prescribe how plan or programme proponents should respond to the findings of an environmental assessment; instead the assessment findings (as documented in the "environmental report") should be "taken into account" during the preparation of the plan or programme and the project can be executed though some significant negative effects remain.

However both assessments are related from the procedural point of view and can be performed as an integrated procedure under condition that in the EIA/SEA study the AA (Croatian NIA procedure, see below Croatian Appropriate Assessment approach ) is clearly identified as separate part, which is common practice in many European countries.