This dataset comprises of suspended sediment, sediment transport and water column structure data collected at two sites in the mouth of the Dee Estuary, Liverpool Bay during February and March of every year from 2005 to 2009. Throughout each data collection cruise the RV Prince Madog underway monitoring system recorded latitude, longitude, ship speed and heading, depth, air temperature, air pressure, humidity, wind speed and direction, photosynthetically active radiation (PAR), sea temperature and salinity, beam transmission, fluorescence and, for 2009, dissolved oxygen concentration. At each site visit profiles of the water column were made over a 25 hour tidal cycle using a conductivity-temperature-depth (CTD) sensor package. Measurements include temperature, salinity, PAR, beam attenuation, particle scattering and transmission, fluorescence, and oxygen concentration. Additionally samples of salinity, suspended particulate matter and in-situ temperature at discrete depths within the water column were obtained and grab samples were taken from the sea-bed after each CTD cast. The RV Prince Madog also performed side-scan sonar tows. During the February cruises mooring frames were deployed on the sea-bed. These frames provided current profiles, particle size information, particle scattering information, bed ripple profiles, sediment settling velocity and temperature, salinity and pressure at each site. The mooring frames were recovered during the March cruises. The main aim of this research was to assess and advance the latest marine sediment transport models. These data allow this assessment to be made by providing information on the complex inter-dependence of sediment processes in the bottom boundary layer. The data were collected by the Proudman Oceanographic Laboratory (now the National Oceanography Centre). Data management was provided by the British Oceanographic Data Centre.