Whey protein isolate (WPI) was mixed with anionic flaxseed (Linum usitatissimum L.) gum (FG), and phase transition during coacervate formation was monitored. Effects of ionic strength and hydrogen bonding on coacervation of WPI‐FG system and corresponding rheological properties were investigated. During coacervate formation, structural transitions were confirmed by both turbidimetry and confocal laser scanning microscopy. Increasing ionic strength with sodium chloride (50 mM) decreased optical density (600 nm) at pHmax. Correspondingly, pHc and pHϕ1 decreased from pH 5.4 to 4.8 and from 5.0 to 4.6, respectively, while pHϕ2 increased from pH 1.8 to 2.4. Sodium chloride suppressed biopolymer electrostatic interactions and reduced coacervate formation. Adding urea (100 mM) shifted pHϕ1, pHmax, and pHϕ2 from 4.8, 3.8, and 1.8 to 5.0, 4.0, and 2.2, respectively, while pHc was unaffected. Optical density (600 nm) at pHmax (0.536) was lower than that of control in the absence of urea (0.617). This confirmed the role of hydrogen bonding during coacervate formation in the biopolymer system composed of WPI and FG. Dynamic shear behavior and viscoelasticity of collected coacervates were measured, and both shear‐thinning behavior and gel‐like properties were observed. Addition of sodium chloride and urea reduced ionic strength and hydrogen bonding, resulting in decreased WPI‐FG coacervate dynamic viscosity and viscoelasticity. The disturbed charge balance contributed to a loosely packed structure of coacervates which were less affected by altered hydrogen bonding. Findings obtained here will help to predict flaxseed gum behavior in protein‐based foods.