The water extract of Lepidium coronopus (L.); Al-Shehbaz (syn. Coronopus squamatus (Forrsk.) Asch); (LCWE) was subjected to phytochemical investigation using HPLC-ESI-MS analysis. Thirteen flavonoid derivatives were detected. Nine kaempferol glycoside and acyl derivatives were identified, in addition to two quercetin and two isorhamnetin glycosides. Among the identified compounds, 8 and 12 (kaempferol-di-O-glucoside-sinapoyl acetate isomers) are newly identified natural products and were firstly identified in the current study using LC-MS technique. LCWE was evaluated for its anti-inflammatory potential in vivo. It showed significant inhibition of the carrageenan induced hind rat paw edema, showing potencies 78.5%, 78.5%, and 89.3% at 100, 200, and 300 mg/kg, respectively. Meanwhile, the effects of LCWE on PGE2, TNF-ɑ, and MPO production in the inflamed paw exudate were measured. Central and peripheral analgesic activities were evaluated by hot plate and writhing techniques. LCWE protected mice against acetic acid-induced writhing by 28.2%, 37.0%, and 54.2% at 100, 200, and 300 mg/kg. LCWE peripheral analgesia was stronger than central effect. LCWE also inhibited RANKL stimulated TRAP activity in RAW264 cells completely at 50 and 20 µg/mL without any significant cytotoxicity to RAW264 macrophages. The metabolomic profile of LCWE explained its biological activities. Furthermore, the identified flavonoid constituents have strong chemosystematic significance confirming the change of nomenclature from the genus Coronopus to the genus Lepidium.