In places where there are rivers and lakes,students usually

1.in places where there are rivers and lakes,此为地点状语从句
2.by boat 是固定搭配,by+交通工具,代表乘该交通工具,如by car,就是开车的意思.
3.In Japan,most students takes trains to school.
如果按第二条来处理,即：In Japan,most students go to school by train.
这就是他们的区别.