The origins of the Zeche Walsum lie in August Thyssen's acquisition of multiple coalfield areas north of Duisburg-Hamborn from the 1880s onward. In 1903 a portion of the field of the Grubenfeld Deutscher Kaiser was separated and the Gewerkschaft Rhein I founded. In 1904 plans were laid to develop the field with a double-shaft installation, and Thyssen submitted an operating plan to the mining authority, which was approved in the same year. Preliminary sinking of a shallow test shaft followed in 1904, but true shaft sinking was repeatedly delayed. Problems with land purchases for surface installations postponed the start of sinking until 1914, and the First World War then suspended work entirely.
In 1921, following the acquisition by the family Thyssen-Bornemisza, the Gewerkschaft Walsum was founded to develop the mine independently. The Ruhr occupation by French troops in 1923 interrupted these efforts again. After the resolution of field ownership questions with the Vereinigte Stahlwerke AG, shaft sinking for Schacht 1 resumed in 1927 using the freezing method. In 1929 the shaft reached the coal measures at 339 metres, but a water inrush forced a temporary halt. Sinking of Schacht 2 began in 1930 and the shaft reached the Carboniferous in the same year. During 1930, production for the mine's own use also commenced. The economic crisis of 1931–1932 severely curtailed activity.
After resumption of work in 1933, the provisional final depth of 850 metres was reached by 1935. Construction of the surface installations had begun in 1930 with the mine's own power station. The harbour basin — the Nordhafen Walsum — was laid out from 1933 to 1936, connecting the colliery directly to the Rhine for coal shipment. A mine ventilation fan was installed in 1934. In 1935, the fourth level was established in Schacht 1 at 800 metres depth. In 1936 Schacht 2 connected to the fourth level. From June 1939 the main regular extraction began using four-level winding frames with large-capacity wagons of 3,800 litres. In 1937–1939 the distinctive tower headframe over Schacht 1 — the Franz-Lenze-Schacht — was erected, reaching 70 metres in height; some sources give the completion as 1937, others indicate the full finishing of this structure by 1939. The tower headframe over Schacht 1 was built in reinforced concrete, a relatively rare material for such structures in the Ruhrgebiet at the time, and was designed to accommodate the extremely high extraction capacity planned for the installation. A matching ventilation building with fan and diffuser dating from 1934 completed the principal surface complex. In 1941 a section of the Kaue (pithead bath building) was completed.
The colliery sustained damage near the end of the Second World War from artillery fire as Allied forces approached, and operations were suspended in 1945. After only three months of standstill, the mine resumed in June 1945. In post-war reconstruction the Gewerkschaft Walsum was reconstituted as the Walsum Bergbau Aktiengesellschaft. From 1954 to 1955, Schacht 2 was fully equipped as a second winding shaft. It received a tower headframe matching in design that of Schacht 1, and was equipped with skip hoisting. By 1956 Schacht 2 was in operation as a second production shaft. The two shafts subsequently received their official names: Schacht 1 became the Franz-Lenze-Schacht, named after an engineer prominent in coking gas technology and in the development of the Thyssen gas network; Schacht 2 became the Wilhelm-Roelen-Schacht, named after the first works director of the mine.
In 1966 the fifth level was established in a blind shaft from the third level at 913 metres depth. In the same year Augermining was applied for the first time in the Ruhr coalfield, in the E/F seam horizon at the Zeche Walsum. Also in 1966, the winding installation at the Wilhelm-Roelen-Schacht was converted to skip hoisting. In 1967 further deepening work was carried out on the Franz and Wilhelm shafts. In 1968 the Walsum Bergbau Aktiengesellschaft passed from the private ownership of the family Thyssen-Bornemisza into the newly founded Ruhrkohle AG. In the same year the Franz and Wilhelm shafts connected to the fifth level. Production was fully mechanised in subsequent years.
In 1976 the Schachtanlage Wehofen 1/2 was taken over from the closed Zeche Friedrich Thyssen 2/5; the Wehofen shafts served solely for water management. From 1979 preparatory works began for a new shaft, Schacht Voerde, located eight kilometres north-west of the main Walsum 1/2 installation. Freezing works for Schacht Voerde began in 1980, with a freezing column of 627 metres. The actual shaft sinking began in 1981. In 1987 Schacht Voerde entered service as an external shaft for ventilation and man-riding in the northern field. In 1989 the daily raw coal output at the mine reached 24,500 tonnes.
The Bergwerk Rheinland was closed in 1993, after which Bergwerk Walsum was assigned a larger extraction area under the Rhine, absorbing the shafts Rheinpreußen 8, Rheinpreußen 9, and Rheinberg from the former Bergwerk Rheinland. In exchange the Wehofen shafts were relinquished. After extraction of the coal reserves in the former Rheinpreußen field was completed, Schacht Rheinpreußen 9 was backfilled and abandoned in 2001 and Schacht Rheinpreußen 8 in 2004. On 30 August 2005 the state government announced the closure of the mine for mid-2008, partly due to contested plans to work reserves under the Rhine, which raised fears of dyke subsidence. The extraction headframes, winding engine houses, and the 1943 ventilation building were listed as protected monuments in the same year.
The last coal was raised at the Zeche Walsum on 27 June 2008, ending mining in the city of Duisburg and making it the last Duisburg colliery to close. Over nearly 69 years, approximately 159 million tonnes of coal had been produced, with around 3,000 employees in the final years. On 3 May 2013 the headframe of Schacht Voerde was demolished by controlled explosion, completing the clearance of that shaft site, which was subsequently returned to agricultural use.
From 2011 the Ruhrkohle AG applied to the city of Duisburg for permission to demolish the protected buildings of the main site on economic grounds, and by 2015 the RAG still maintained its preference for demolition. The great majority of the colliery buildings were demolished. However, following public protests, the tower headframe of Schacht 1 (the Franz-Lenze-Schacht) was retained as a local landmark and is listed as a protected monument. Schacht 2's headframe was shortened to 41.8 metres and converted into one of the main sites of the centralised mine-water management system (Ewigkeitskosten — the permanent post-mining obligations). The Zeche Walsum is a listed site on the Route der Industriekultur, Themenroute 3 (Duisburg: Industriekultur am Rhein). The adjacent Kraftwerk Duisburg-Walsum continued in operation, expanded by a new generating block in 2007.