In the case of Naimittika pralaya, after Brahma's daytime, a dreadful drought occurs for 100 years. Then the sun changes into 7 suns and burns the lower realms, bhuloka, and also the upper realms till mahar loka. Then rain pours down for 100 years and completely floods the lower, middle and upper realms. In short, the whole universe is filled with water.
In the case of Prakrtika pralaya, after Brahma's death, the destruction that follows is similar to the Naimittika pralaya. First there would be a drought for 100 years. Then the sun with its heat would burn all the lokas of the universe. The next 100 years winds would turn the skies gray with dust. Then for the next 100 years rain will pour down and fill the universe with water.
Correct me if i'm wrong but here i don't see any major difference between the two types of pralayas. The only difference i see is that, in the first case, the destruction happens at the end of a kalpa. And in the second case, the destruction happens after the death of Brahma. But the nature of destruction in both the case is similar.