Why there was no civilization in Mississippi delta and Parana delta,if these places had good conditions for agriculture and civilization?

They're not exactly at the river mouth, but the Guarani people are one of the major linguistic groups of Latin America and their's is still the most spoken language in Paraguay. They had a well developed culture well before the Europeans came along and a lot of it survives today.

I'm not sure why the lower Parana and river plate region wasn't more settled, but I can tell you that it is a very slow moving river, most of it only 1 or 2 meters deep, and it carries enormous amounts of sediment. So it's borders would move constantly before it was built upon, and even today a lot of the delta region is underdeveloped because it is so flood prone. In the past 10-20 years people have started building on the flood plain and cultivating rice, but this is still at risk of flooding and requires a lot of investment.

Historically the province of Entre Rios was the biggest cattle producer of Argentina (because they can be moved around when it floods), so maybe it was hard to colonize before the Europeans because there were no native domestic grazing animals. To this day you still hear of flooding so severe in this province that people's animals drown because there aren't enough ferries, or even dry land, to move them onto.