A method for maintaining flow control in a buffer memory coupled to a storage controller is provided. The storage controller includes, first and second counters that are used to monitor when data is read from a buffer memory and when data is transferred from the buffer memory to the host. The method includes, incrementing first and second counter values when data is placed in the buffer memory; decrementing a first counter value when data is read from the buffer memory; and decrementing the second counter value when data is sent to a host. The method further includes, pausing a first channel logic between a transport module and a storage disk when there is no data in the buffer memory; and pausing a second channel logic between a disk and the buffer memory if there is no space in the buffer memory.