Instructions
Travel towards Ecruteak City by going down Route 37. Before you reach the city, go east onto route 42. Down this road you will find the cave entrance of Mt. Mortar.
Enter the cave of Mt. Mortar. Marill is in the front room of the cave.
Walk around the front room until you randomly run into a Marill. The Pokemon is incredibly rare, with only a 1% encounter rate, so you may not run into one for a significant amount of time.
Battle Marill until its Hit Points (HP) are low and its HP bar turns red, and then catch it by throwing a Poke Ball. Like most other Water-type Pokemon, Marill is especially weak against Grass and Electric-type Pokemon, but it is resistant to Steel, Fire, Water and Ice-type Pokemon.