Actually, no Waterball through Energy Admixture or Energy Substitution. It'd have to be an Acidball or Coldball at best, because Water isn't an energy type, let alone one of those allowed by those two feats.
Masters of the Wild has an optional rule to let folks increase their animal companions' Hit Dice through a ritual that costs some XP and stuff, but it doesn't give them all the boosts that 3.5 animal companions get; they're just normal animals (and you could have lots of them with fewer individual HD), that you might use a ritual to advance along its natural hit die progression with normal animal HD-based benefits from those like any other animal. And I don't think the DM would allow a 3.5 supplement like PHB 2 in a 3.0 game, but who knows? Also, note that 3.0 druids cannot cast spontaneous Summon Nature's Ally spells.
Clerics can be brutal fighting machines. The 4th-level cleric spell (also on the War Domain, and the Hero Domain as well for Shamans) Divine Power gives the cleric a fighter's BAB and HP for a while, and Righteous Might (also on the same spell lists, along with the Strength Domain list and the Water Shugenja spell list), a 5th-level spell, makes the cleric one size larger and gives them higher Strength for a while. Clerics have Searing Light and Flame Strike on their spell list, of course, which are good for blasting. With the Water and War domains, they'd have a bit more ranged-damage spellcasting.
Shamans get Ancestral Vengeance instead of Searing Light, but a Shaman with the Hero or War domain, and the River or Fury domain, would fit well enough. Unfortunately, Shamans get fewer proficiencies than Clerics, but that does mean they would benefit more from a dip into 1, 2, or 4 levels of Fighter (preferably 1 or 2, since 4 would cut into your spellcasting a lot).
A fighter 1/sorcerer (or wizard) 9/Spellsword 10 would cast spells as per a 14th-level sorcerer or wizard (7th-level spells, like Mordenkainen's Sword, Prismatic Spray, Finger of Death, Bigby's Grasping Hand, and Delayed Blast Fireball), while being slightly less tough than a cleric. The only supplement this requires is Tome & Blood. If going Wizard, it should be an Evoker for blasting, or Transmuter for buffing. Also, note that the 6th-level Transmutation spell Tenser's Transformation can make you a tougher, more effective warrior, though it prevents you from casting spells while it is active. And Stoneskin is still effective in 3.0, though slightly less than in 3.5 I think (at least at high levels) and much weaker than in 2nd Edition AD&D (in which it was awesome). But on the other hand, Protection from Arrows is better in 3.0 than it is in 3.5.
I own all WotC 3.0 books (not PDFs) except for a few of the FR books (basically the regional ones), Book of Vile Darkness (IIRC it came out at the end of 3.0, and I oppose its use of "vile" content on moral grounds), and Enemies & Allies because it would be useless to me. Mystic Theurge is not in 3.0. Period. Fact. Nor is Eldritch Knight, Horizon Walker, or Thaumaturgist. Horizon Walker was loosely based on the King/Queen of the Wild from Masters of the Wild. Thaumaturgist may have some small resemblance to the Incantrix from Magic of Faerun. Eldritch Knight is a lame substitute for the Spellsword from Tome & Blood. Mystic Theurge is a lame substitute for the Geomancer from Masters of the Wild.
A fixed Spellsword, fixed Geomancer, and so on could have been used in core 3.5 rather than the utterly flavorless "prestige" classes they threw in. Or they could have just fixed multiclassing (gasp! shock!) and/or put in a few simple feats to handle that, rather than pointlessly changing so many feats and spells and other things that weren't broken in the first place. Not to say 3.5 didn't fix a few things, but honestly, most of it was wasted effort that changed or broke things that were fine or at least acceptable in 3.0 (like druids, who were strong in 3.0 but not nearly as broken as 3.5 made them, especially by including Natural Spell in the core when it had previously been one of the more-broken supplemental options in Masters of the Wild, pretty much the most-poorly-vetted supplement before 3.5). Instead, things like Practiced Caster and such didn't come out until later supplements.