In Dutch, in is used for locations inside enclosed spaces: in de kamer, in Amsterdam, in het water. Op means on a surface or at a location that is more open: op de tafel, op straat, op het plein, op school. The distinction between in de stad (inside the city) and op het plein (on the open square) reflects the enclosed versus open distinction. Op is also used for certain institutions: op kantoor, op school, op de universiteit.
Aan indicates contact with a surface, edge or line: aan de muur (on the wall), aan de rivier (along the riverbank), aan de beurt (it is your turn). Bij means near, at someone’s place or in the vicinity: bij de deur (by the door), bij ons thuis (at our place), bij de bakker (at the baker’s shop). Naast means next to, voor means in front of, achter means behind and tussen means between — these are more straightforward and closer to their English equivalents.
Prepositions with transport follow their own rules. In a car or taxi: in de auto. On public transport: in de bus, in de trein — you are enclosed inside. On a bike or horse: op de fiets, op het paard — you sit on top. These differ from English, which uses on for all vehicles. When uncertain, note the collocations you encounter in reading and build your mental map of each preposition through examples rather than abstract rules.