The main conflict in The Water is Wide is the gap between how Pat Conroy believes he can successfully educate his class and what he's allowed to do by the administration. This conflict comes to a head when he is fired for his style of teaching.
Conroy arrives on Yamacraw Island to find it far more separated from the mainland United States than he expected. The children are far behind their mainland counterparts -- and it doesn't seem like the education administration in South Carolina is particularly concerned with their lack of progress that stems from lack of resources and staff. When he realizes they can't name U.S. presidents or count very high, he knows something has to be done.
When Conroy realizes the students aren't able to learn from traditional teaching methods, he adopts new ways of teaching them. His methods include taking them on trips to South Carolina and Washington DC, watching films, and discussing music. Conroy attempted to motivate the students while teaching them things they'd need to succeed in life.
When the administration disagreed with his methods -- some of which were unorthodox, such as taking part-time jobs to supplement travel expenses for the students -- he was fired. Despite protests and a court case, Conroy never got his teaching job back. He agrees that in the end, he should have paid more attention to the demands of the administration. However, his method was one that was getting results -- unlike what had been tried before.
Conroy's story is set against a backdrop of the struggle for Civil Rights in America. The children he teaches are largely black and poor -- and he knows the conditions they learn in wouldn't be deemed acceptable for white students. Industrial pollution is threatening the livelihood of the community and the lack of education makes it difficult to prepare the students for other work in the future.